Low‐coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

Multiple parapatric pollinators have radiated across a continental fig tree displaying clinal genetic variation

(2019) Hui Yu et al.   MOLECULAR ECOLOGY

A temperate pollinator with high thermal tolerance is still susceptible to heat events predicted under future climate change

(2018) Timothy L. Sutton et al.   ECOLOGICAL ENTOMOLOGY

Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns

(2018) Harald Ringbauer et al.   GENETICS

Whole-genome data reveal the complex history of a diverse ecological community

(2018) Lynsey Bunnefeld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns

(2018) Harald Ringbauer et al.   GENETICS

Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model

(2017) Rui J. Costa et al.   GENETICS

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Tournament ABC analysis of the western Palaearctic population history of an oak gall wasp, Synergus umbraculus

(2017) Graham N. Stone et al.   MOLECULAR ECOLOGY

Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems

(2017) Crispin Y. Jordan et al.   MOLECULAR ECOLOGY

Population-genomic inference of the strength and timing of selection against gene flow

(2017) Simon Aeschbacher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model

(2017) Rui J. Costa et al.   GENETICS

Lines in the land: a review of evidence for eastern Australia's major biogeographical barriers to closed forest taxa

(2016) Litticia M. Bryant et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

A performance study of the impact of recombination on species tree analysis

(2016) Zhiwei Wang et al.   BMC GENOMICS

Para-allopatry in hybridizing fire-bellied toads (Bombina bombinaandB. variegata): Inference from transcriptome-wide coalescence analyses

(2016) Beate Nürnberger et al.   EVOLUTION

Geographic structuring into vicariant species-pairs in a wide-ranging, high-dispersal plant–insect mutualism: the case of Ficus racemosa and its pollinating wasps

(2016) A. Bain et al.   EVOLUTIONARY ECOLOGY

Genome-wide sequence data suggest the possibility of pollinator sharing by host shift in dioecious figs (Moraceae,Ficus)

(2016) Nakatada Wachi et al.   MOLECULAR ECOLOGY

One step ahead: a parasitoid disperses farther and forms a wider geographic population than its fig wasp host

(2016) Timothy L. Sutton et al.   MOLECULAR ECOLOGY

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi

(2015) Li-Hua Niu et al.   BMC MICROBIOLOGY

The incidence and pattern of copollinator diversification in dioecious and monoecious figs

(2015) Li-Yuan Yang et al.   EVOLUTION

Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent

(2015) K. Lohse et al.   GENETICS

Evolutionary and contemporary responses to habitat fragmentation detected in a mesic zone marsupial, the long-nosed potoroo (Potorous tridactylus) in south-eastern Australia

(2015) Greta. J. Frankham et al.   JOURNAL OF BIOGEOGRAPHY

Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism

(2015) Enwei Tian et al.   MOLECULAR ECOLOGY

Movements of genes between populations: are pollinators more effective at transferring their own or plant genetic markers?

(2015) M. Liu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Molecular species delimitation of a symbiotic fig-pollinating wasp species complex reveals extreme deviation from reciprocal partner specificity

(2014) Clive T Darwell et al.   BMC EVOLUTIONARY BIOLOGY

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

(2014) Konrad Lohse et al.   GENETICS

Pleistocene climate fluctuations influence phylogeographical patterns inMelomys cervinipesacross the mesic forests of eastern Australia

(2014) Litticia M. Bryant et al.   JOURNAL OF BIOGEOGRAPHY

Estimation of the Spontaneous Mutation Rate in Heliconius melpomene

(2014) Peter D. Keightley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Aridification drove repeated episodes of diversification between Australian biomes: Evidence from a multi-locus phylogeny of Australian toadlets (Uperoleia: Myobatrachidae)

(2014) Renee A. Catullo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

How to be a fig wasp down under: The diversity and structure of an Australian fig wasp community

(2013) Simon T. Segar et al.   ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family

(2013) Peter D. Keightley et al.   GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Divergent lineages in two species ofDendrobiumorchids (D. speciosumandD. tetragonum) correspond to major geographical breaks in eastern Australia

(2013) Jacinta M. Burke et al.   JOURNAL OF BIOGEOGRAPHY

Patterns of rain forest plant endemism in subtropical Australia relate to stable mesic refugia and species dispersal limitations

(2013) Lui C. Weber et al.   JOURNAL OF BIOGEOGRAPHY

Mountain barriers and river conduits: phylogeographical structure in a large, mobile lizard (Varanidae:Varanus varius) from eastern Australia

(2013) Peter J. Smissen et al.   JOURNAL OF BIOGEOGRAPHY

The biogeographical boundaries of northern Australia: evidence from ecological niche models and a multi-locus phylogeny ofUperoleiatoadlets (Anura: Myobatrachidae)

(2013) Renee A. Catullo et al.   JOURNAL OF BIOGEOGRAPHY

Likelihood-based inference of population history from low-coveragede novogenome assemblies

(2013) Jack Hearn et al.   MOLECULAR ECOLOGY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Dioecy, more than monoecy, affects plant spatial genetic structure: the case study ofFicus

(2013) Alison G. Nazareno et al.   Ecology and Evolution

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome

(2013) Jin-Hua Xiao et al.   GENOME BIOLOGY

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Human-induced versus historical habitat shifts: identifying the processes that shaped the genetic structure of the threatened grassland legless lizard, Delma impar

(2012) Susana P. Maldonado et al.   CONSERVATION GENETICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Effects of historical forest contraction on the phylogeographic structure of Australo-Papuan populations of the red-legged pademelon (Macropodidae: Thylogale stigmatica)

(2011) PEGGY MACQUEEN et al.   AUSTRAL ECOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia

(2011) David G Chapple et al.   BMC EVOLUTIONARY BIOLOGY

A General Method for Calculating Likelihoods Under the Coalescent Process

(2011) K. Lohse et al.   GENETICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny and historical biogeography of ancient assassin spiders (Araneae: Archaeidae) in the Australian mesic zone: Evidence for Miocene speciation within Tertiary refugia

(2011) Michael G. Rix et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Ficus racemosa is pollinated by a single population of a single agaonid wasp species in continental South-East Asia

(2010) N. KOBMOO et al.   MOLECULAR ECOLOGY

Phylogenetics of the pademelons (Macropodidae: Thylogale) and historical biogeography of the Australo-Papuan region

(2010) Peggy Macqueen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Outbreeding and possibly inbreeding depression in a pollinating fig wasp with a mixed mating system

(2009) J M Greeff et al.   HEREDITY

Wind-borne insects mediate directional pollen transfer between desert fig trees 160 kilometers apart

(2009) S. Ahmed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence?

(2008) FRISO P. PALSTRA et al.   MOLECULAR ECOLOGY

Distribution and phylogenetic relationships of Australian glow-worms Arachnocampa (Diptera, Keroplatidae)

(2008) Claire H. Baker et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny, biogeography, and ecology of Ficus section Malvanthera (Moraceae)

(2008) Nina Rønsted et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evidence for multiple refugia at different time scales during Pleistocene climatic oscillations in southern Australia inferred from phylogeography

(2008) M BYRNE   QUATERNARY SCIENCE REVIEWS

Marine isotope stage 3 sea level fluctuations: Data synthesis and new outlook

(2008) M. Siddall et al.   REVIEWS OF GEOPHYSICS